diff --git a/pybis/src/python/pybis/attribute.py b/pybis/src/python/pybis/attribute.py
index 0ac40c5e09efc7315f120c2074495a31e9e1e410..6d01ebf9f853361bdc34d5e73e0d67dac949ed32 100644
--- a/pybis/src/python/pybis/attribute.py
+++ b/pybis/src/python/pybis/attribute.py
@@ -106,6 +106,10 @@ class AttrHolder():
new_obj['typeId'] = self._type['permId']
continue
+ elif attr == 'kind':
+ # when creating a new dataset, the attribute «kind» is called «dataSetKind»
+ new_obj['dataSetKind'] = self._kind
+
elif attr == 'attachments':
attachments = getattr(self, '_new_attachments')
if attachments is None:
diff --git a/pybis/src/python/pybis/dataset.py b/pybis/src/python/pybis/dataset.py
index 0dc26a232dd3f74622f8913b48712feef3a1a7d4..5c18c4f0dbb348f97fba14ecfc2631603c8455e6 100644
--- a/pybis/src/python/pybis/dataset.py
+++ b/pybis/src/python/pybis/dataset.py
@@ -17,7 +17,31 @@ class DataSet(OpenBisObject):
""" DataSet are openBIS objects that contain the actual files.
"""
- def __init__(self, openbis_obj, type=type, data=None, files=None, folder=None, props=None, **kwargs):
+ def __init__(self, openbis_obj, type=type, data=None, files=None, folder=None, kind=None, props=None, **kwargs):
+
+ if kwargs is None:
+ kwargs = {}
+
+ if kwargs.get('code'):
+ kwargs["autoGeneratedCode"] = False
+ else:
+ kwargs["autoGeneratedCode"] = True
+
+ if kind == 'PHYSICAL_DATA':
+ if files is None:
+ raise ValueError('please provide at least one file')
+
+ if isinstance(files, str):
+ files = [files]
+
+ for file in files:
+ if not os.path.exists(file):
+ raise ValueError('File {} does not exist'.format(file))
+
+
+ self.__dict__['files'] = files
+
+ # initialize the attributes
super(DataSet, self).__init__(openbis_obj, type, data, props, **kwargs)
self.__dict__['files_in_wsp'] = []
@@ -31,9 +55,15 @@ class DataSet(OpenBisObject):
self.__dict__['shareId'] = data['physicalData']['shareId']
self.__dict__['location'] = data['physicalData']['location']
- # new DataSet
- if files is not None:
- self.__dict__['files'] = files
+
+ if kind is not None:
+ kind = kind.upper()
+ allowed_kinds = ['PHYSICAL_DATA', 'CONTAINER', 'LINK']
+ if kind not in allowed_kinds:
+ raise ValueError(
+ "only these values are allowed for kind: {}".format(allowed_kinds)
+ )
+ self.a.__dict__['_kind'] = kind
self.__dict__['folder'] = folder
@@ -391,41 +421,67 @@ class DataSet(OpenBisObject):
def save(self):
+
if self.is_new:
- if self.files is None or len(self.files) == 0:
- raise ValueError('Cannot register a dataset without a file. Please provide at least one file')
+ datastores = self.openbis.get_datastores()
+ permId = None
if self.sample is None and self.experiment is None:
raise ValueError('A DataSet must be either connected to a Sample or an Experiment')
- # upload the data to the user session workspace
- datastores = self.openbis.get_datastores()
-
- self.upload_files(
- datastore_url= datastores['downloadUrl'][0],
- files=self.files,
- folder='',
- wait_until_finished=True
- )
-
- # activate the ingestion plugin, as soon as the data is uploaded
- request = self._generate_plugin_request(dss=datastores['code'][0])
-
- resp = self.openbis._post_request(self.openbis.reg_v1, request)
-
- if resp['rows'][0][0]['value'] == 'OK':
- permId = resp['rows'][0][2]['value']
- if permId is None or permId == '':
- self.__dict__['is_new'] = False
- if VERBOSE: print("DataSet successfully created. Because you connected to an openBIS version older than 16.05.04, you cannot update the object.")
+ if self.kind == 'PHYSICAL_DATA':
+ if self.files is None or len(self.files) == 0:
+ raise ValueError(
+ 'Cannot register a dataset without a file. Please provide at least one file'
+ )
+
+ # for uploading phyiscal data, we first upload it to the session workspace
+ self.upload_files(
+ datastore_url= datastores['downloadUrl'][0],
+ files=self.files,
+ folder='',
+ wait_until_finished=True
+ )
+
+ # activate the ingestion plugin, as soon as the data is uploaded
+ # this will actually register the dataset in the datastore and the AS
+ request = self._generate_plugin_request(dss=datastores['code'][0])
+ resp = self.openbis._post_request(self.openbis.reg_v1, request)
+ if resp['rows'][0][0]['value'] == 'OK':
+ permId = resp['rows'][0][2]['value']
+ if permId is None or permId == '':
+ self.__dict__['is_new'] = False
+ if VERBOSE: print("DataSet successfully created. Because you connected to an openBIS version older than 16.05.04, you cannot update the object.")
+ else:
+ new_dataset_data = self.openbis.get_dataset(permId, only_data=True)
+ self._set_data(new_dataset_data)
+ if VERBOSE: print("DataSet successfully created.")
+ return self
else:
- new_dataset_data = self.openbis.get_dataset(permId, only_data=True)
- self._set_data(new_dataset_data)
- if VERBOSE: print("DataSet successfully created.")
+ raise ValueError('Error while creating the DataSet: ' + resp['rows'][0][1]['value'])
+ # CONTAINER
else:
- raise ValueError('Error while creating the DataSet: ' + resp['rows'][0][1]['value'])
+ if self.files is not None and len(self.files) > 0:
+ raise ValueError(
+ 'DataSets of kind CONTAINER or LINK cannot contain data'
+ )
+ request = self._new_attrs()
+ props = self.p._all_props()
+ DSpermId = datastores['code'][0]
+ request["params"][1][0]["properties"] = props
+ request["params"][1][0]["dataStoreId"] = {
+ "permId": DSpermId,
+ "@type": "as.dto.datastore.id.DataStorePermId"
+ }
+ resp = self.openbis._post_request(self.openbis.as_v3, request)
+
+ if VERBOSE: print("DataSet successfully created.")
+ new_dataset_data = self.openbis.get_dataset(resp[0]['permId'], only_data=True)
+ self._set_data(new_dataset_data)
+ return self
+ # updating the DataSEt
else:
request = self._up_attrs()
props = self.p._all_props()
diff --git a/pybis/src/python/pybis/definitions.py b/pybis/src/python/pybis/definitions.py
index 6ccd5ddb2d494faba0795044b881072308a90512..9371574023d18ea5860339fe5270652d28e017a3 100644
--- a/pybis/src/python/pybis/definitions.py
+++ b/pybis/src/python/pybis/definitions.py
@@ -63,8 +63,8 @@ def openbis_definitions(entity):
"multi": "parents children components tags attachments".split(),
},
"DataSet": {
- "attrs_new": "type kind experiment sample parents children components containers tags".split(),
- "attrs_up": "kind parents children experiment sample components containers tags".split(),
+ "attrs_new": "type code autoGeneratedCode kind experiment sample parents children components containers tags".split(),
+ "attrs_up": "parents children experiment sample components containers tags".split(),
"attrs": "code permId type kind experiment sample parents children components containers tags accessDate dataProducer dataProductionDate registrator registrationDate modifier modificationDate dataStore size measured".split(),
"ids2type": {
diff --git a/pybis/src/python/pybis/pybis.py b/pybis/src/python/pybis/pybis.py
index 16212f4e5a2aaf0a6344edad65127dee84c1f21a..2d4a15ae0ec067afc14ee38c01ccf796f5f51ab1 100644
--- a/pybis/src/python/pybis/pybis.py
+++ b/pybis/src/python/pybis/pybis.py
@@ -2783,21 +2783,13 @@ class Openbis:
new_object = new_sample # Alias
- def new_dataset(self, type=None, files=None, props=None, folder=None, kind='PHYSICAL_DATA', **kwargs):
+ def new_dataset(self, type=None, kind='PHYSICAL_DATA', files=None, props=None, folder=None, **kwargs):
""" Creates a new dataset of a given sample type.
"""
- if files is None:
- raise ValueError('please provide at least one file')
- elif isinstance(files, str):
- files = [files]
-
- for file in files:
- if not os.path.exists(file):
- raise ValueError('File {} does not exist'.format(file))
type_obj = self.get_dataset_type(type.upper())
- return DataSet(self, type=type_obj, files=files, folder=folder, props=props, **kwargs)
+ return DataSet(self, type=type_obj, kind=kind, files=files, folder=folder, props=props, **kwargs)
def new_semantic_annotation(self, entityType=None, propertyType=None, **kwargs):
""" Note: not functional yet. """
@@ -2836,7 +2828,6 @@ class Openbis:
return dss[dss['code'] == dss_code]['downloadUrl'][0]
-
class LinkedData():
def __init__(self, data=None):
self.data = data if data is not None else []